Yayyyy! The most famous line of the sum summer, the water's fine, come on in? Well, not necessarily. People told not to drink the water or get in. Tonight, the "20/20" test. Cecilia Vega armed with a test kit. And the results are in. Reporter: Ah, sweet summer -- the time of year when we get back in touch with our more amphibious aspirations. Of course, this means close contact with mother nature's most notorious nuisances -- sharks. Alligators. Jellyfish. Now, attacks from creatures lurking in the dark depths are serious but they aren't nearly as common as attacks from the stuff inside the water that we can't see. There is a whole bunch of urban slobber from the upper watershed that makes its way down, and then flows onto the beach. Reporter: Steve fleischli works for the natural resources defense council. Throw in the mix, horse and bird poop, and it sort of makes a witch's brew of contamination at these beaches. Reporter: Blech. And that bacterial brew may be bubbling where we least expect it. Let's start our magical misery tour. Right here at the malibu pier beach in California, smack in the middle of wealth and glamour. This beach, malibu pier, is considered a repeat offender. Time after time scientists have found bacteria in this water right here where you can see children are playing, surfers are surfing. We're going to take some samples and find out how dirty it really is. We packed our sample bottles in a cooler and headed for a lab. We wait for the results knowing this water could be teeming with bacteria. But that's not stopping anyone from diving in. Now, most beaches post warnings if bacteria counts are too high and even shut them down if the counts are out of control. But that could be too late for some swimmers. We surf all over the world and this is one of the only places where we are getting sick. It's kind of a bummer to hear that there is fecal matter. When you swim in contaminated water, there is a grim inventory of diseases that can be associated with that. From stomach flu, to pink eye, to ear infection, to eye infection, to -- Reporter: Okay, Steve, we get the picture. Malibu pier is in good company. The list of the worst bacteria infested beaches spans the country and sickness abounds from coast to coast. Our next stop, horseshoe lake in Washington state. It might look like the perfect spot to take a summer dip but last month swimmers there found out what really lies below the surface the hard way. A summer scare -- The calls were coming one after another after another. We had 82 reported. 82 reported phone calls. Yeah. Wow. Reporter: Families ended up praying to the porcelain gods. Do you remember what you felt like? I felt like a piece of poop. My stomach, it started to, like twist and turn. Reporter: But I didn't end there. My uncle got sick. My friend Damon got sick. Her dad got really sick, too. You guys are dropping like flies. Oh my gosh, yeah, it was like the movie bridesmaids. Reporter: And like the movie -- Some of them thought they ate something bad. But we don't know if it isn't an E. Coli outbreak, a leaky sewer line, toxic algae. We don't know for sure. Reporter: But it was none of those things. The final tally of suffering swimmers soared past 300. Lab test results confirmed Jim zimny's strongest hunch. The very same bug that has notoriously spread from person to person on cruise trips from hell -- More than 600 fell ill. Reporter: Was deep inside this lake too -- the dreaded norovirus. One person who went into this water behind you was sick, and now hundreds of people suffer because of that? Oh yes. It's very contagious. When people are going in the water, they're basically taking a bath with everybody else who's out there. The problem with viral contamination of the beaches is that they are not sampling most beaches for viruses -- they are sampling for bacteria. Reporter: It seems summer outbreaks are popping up as often as a bad sunburn. On lake Erie just days ago. Half a million Toledo residents unable to drink water from the tap. Reporter: That's no swimming, no showers, no teeth brushing all because the usually blue waters turned into green sludge. It's from toxic algae that's gotten worse every year thanks to farm fertilizer runoff and leaky septic systems. At Florida beaches last month, authorities issued an alert for flesh eating bacteria. Stay out of the water if you have an open wound or weakened immune system. This nasty stuff occurs naturally in warm salty water, leading to 41 infections in the state last year and 11 deaths. And last year in Little Rock, Arkansas, a day at this water park turned nearly deadly for Kali hardig. All of the sudden the headache just started getting worse. And I knew when her eyes rolled back in her head. I knew something bad was wrong. Reporter: They raced to the emergency room where Kali gets the news -- she is infected with a terrifying brain eating amoeba know as naeglaria. Most likely from the water. It's 99% fatal, 1% survival rate. This is Friday night, they told us she'd be gone by Monday. Reporter: It took a monthlong induced coma but Kali is now one of only three people ever known to survive this very rare infection. Naeglaria grows in fresh water warmed by the summer sun. The good news is, it's not easy for it to enter the human body. So what about those tests we ran for contaminated water at the malibu pier? Well, it's official -- bad bacteria. The good news though -- the levels are so low they won't make you sick. A day at the beach should never lead to a night at the hospital. Reporter: So Steve says, don't go in the water within three days of a heavy rainstorm, you can protect yourself by not dunking your head or allowing water to get into your mouth or nose, and staying out when you have open cuts. Also, if you're sick, do everybody a favor and don't go in the water. Reporter: But it's summer. We get it. It's hot outside. And sometimes those blue waters are too inviting to pass up. No matter what may secretly lurk beneath.

This transcript has been automatically generated and may not be 100% accurate.

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